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Nucleic acids and proteins are the key building blocks of life, yet many essential aspects of their relationship remain enigmatic. The aim of our research is to decipher the fundamental rules behind the interactions between nucleic acids and proteins in crowded environments, understand the impact these interactions have had in shaping life’s evolutionary history and study their role in present-day systems. The central hypothesis behind our research is that direct interactions between nucleic acids and proteins have contributed to the establishment of the universal genetic code and that, in turn, the code can be seen as a Rosetta stone for understanding RNA-protein interactions in general. A corollary of this hypothesis, which we are particularly interested in, is that mRNA coding sequences may be complementary to and bind in co-aligned fashion to their cognate proteins, especially if unstructured.
We use and develop different techniques of computational biology, including molecular dynamics simulations, free energy and entropy calculations and structural bioinformatics methods, in close conjunction with experiment. Moreover, we develop novel methods of what could best be described as physicochemical bioinformatics, an approach to representing, analyzing and comparing biological sequences as physicochemical objects, which they invariably are. By combining rigorous, atomistic description of individual biomolecules with the richness of modern-day proteomic and genomic datasets, we strive to discover new fundamental principles behind the organization of biological matter and explain essential biological phenomena from a quantitative, physicochemical perspective.
Bojan Zagrovic obtained an undergraduate degree in biochemistry from Harvard University and a PhD in biophysics from Stanford University, working with Vijay S. Pande. He was an EMBO postdoc with Wilfred F. van Gunsteren at ETH Zurich and a group leader and scientific director at Mediterranean Institute for Life Sciences in native Croatia. He joined Max Perutz Labs and University of Vienna in 2010.
We have shown that the nucleotide-density profiles of mRNA coding sequences closely match the nucleotide-affinity profiles of their cognate proteins, suggesting that mRNAs and the proteins that they encode may, in general, be physicochemically complementary to each other and bind in a co-aligned fashion, especially if unstructured.
We have recently developed VOLPES, a server for visualizing and comparing sequence profiles of different physicochemical properties of proteins and nucleic acids. VOLPES supports over 600 amino-acid and nucleotide property scales and enables multi-scale detection of patterns that may be inaccessible to standard methods of primary sequence analysis.
We have developed a parallel computational suite for the determination of conformational entropy change in biomolecular interactions from molecular dynamics simulation trajectories and have used it to demonstrate that intramolecular couplings provide a surprisingly constant contribution to the overall conformational entropy change in compact proteins.
RNA-protein interactions in an unstructured context.
Zagrovic, Bojan; Bartonek, Lukas; Polyansky, Anton A
Direct interplay between stereochemistry and conformational preferences in aminoacylated oligoribonucleotides.
Polyansky, Anton A; Kreuter, Mathias; Sutherland, John D; Zagrovic, Bojan
Frameshifting preserves key physicochemical properties of proteins.
Bartonek, Lukas; Braun, Daniel; Zagrovic, Bojan
European Research Council: Short, weakly interacting RNAligands for the development of high-concentration monoclonal antibody therapeutics
Austrian Science Fund: RNA-protein interactions in an unstructured context, 2018
Austrian Science Fund: 2’ vs. 3’ aminoacylation in biological translation
2016-2019: The Group Zagrovic participates in the special Doctoral Program "Integrative Structural Biology" reviewed and funded by the Austrian Science Fund FWF.
Awardee of a "Starting Independent Researcher Grant" from the European Research Council ERC
Project title: “Specific and global aspects of protein interactions”
Systematic identification and functional characterization of transcriptional regulators
The mineralosphere as microhabitat for microbe, mineral and organic matter interaction in soils
Activation and regulation of plant immunity by secreted signaling peptides
Transcription start site selection is environmentally controlled to diversify the proteome in eukaryotes
How evolutionary interplay between sexes can help us define phenotypes and develop drugs
Mining for protein-protein interactions with AlphaFold: Lessons from Genome Maintenance
Title to be announced
The magical Martian Methane mystery and other stories about life on Mars
Probing life at the nanoscale - one molecule at a time
The Underworld of Deep-Sea Hydrothermal Vents
Epigenetic regulation of germline development
Sister chromatid cohesion is mediated by individual cohesin complexes
Origin and evolution of a defensive symbiosis in tortoise leaf beetles
Capturing conformational transitions in the ubiquitin conjugation cascade
18th Microsymposium on RNA Biology
The „Microsymposium on RNA Biology“ is an international conference that brings together young scientists, junior and senior group leaders, and company representatives from all over the world to present and discuss their latest findings in the exciting field of small RNAs and beyond. The Microsymposium was founded in 2005 and has established itself as the major small RNA meeting in Europe. It is organized by the four research institutions IMBA, IMP, GMI and the Max Perutz Labs as well as by the RNA community of the Vienna BioCenter.
Transformation Reactions of Organic Contaminants and Oxygen: From Field Sites to Reaction Mechanisms
Title to be announced
Multiscale plant bioimaging using advanced microscopy
Parthenogenesis, cryptobiosis, and the survival in extreme environmental conditions
Evading ageing: Mitochondrial and proteostatic adaptations in oocytes
Ubiquitin & Friends Symposium 2024
The Ubiquitin & Friends Symposium is an annual international meeting taking place in the beautiful capital of Austria, aiming to bring together scholars from various fields studying ubiquitin/Ubl biology and protein degradation in a personal, family-like atmosphere, as suggested by the name.
Genomes in Rhodnius prolixus symbiotic system
Stem cells, immune evasion and metastasis in colorectal cancer
The evolution and development of mollusc shells
Unraveling the Complexity of Crossover Regulation in C. elegans
Dynamics of 3D Genome Structure and Function
How superworms can help to solve our plastic waste crisis
New players in an old pathway: biology of methanogens of the TACK superphylum
Shaping morphogen gradients: from molecules to tissues and back
Studying stressed cells by in situ structural biology
Exploring Microbial Resilience: Unravelling Escherichia coliand#x27;s Stress Response at the Level of Protein Synthesis
Deep homology and deep diversity: Evolving genetic toolkits for making and sensing light
The evolution of cell type identity and tissue microecology at the fetal-maternal interface
The unanticipated roles of PICIs and phages in bacterial evolution
Origin and diversification of gut-derived organs in chordates
Job's Dilemma for the Genome: Why Bad Things Happen to Good Chromosomes
Connections between carbon and nitrogen cycling in the ocean
Understanding how the DNA-loop-extruding protein complex Condensin folds a chromatinized genome into mitotic chromosomes
From Roads to Rivers? Occurrence and environmental fate of tire and road wear particles and of tire-related chemicals
Striking physiology and cell biology of (marine) environmental microorganisms
Mechanisms controlling maintenance of cohesin dependent loops
Title to be announced